Fig. 2

Analysis and visualization of large-scale spatial transcriptomic and proteomic datasets. a Visualization in both expression (top) and physical (bottom) space of the cell types identified by Giotto Analyzer in the pre-optic hypothalamic merFISH dataset, which consists of 12 slices from the same 3D sample (distance unit = 1 μm). b Heatmap showing the marker genes for the identified cell populations in a, c Visualization in both expression and physical space of two representative slices within the z-orientation (100 μm and 400 μm). d, e Overlay of gene expression in both expression and physical space for the selected slices in c, f. Visualization in both expression (top) and spatial (bottom) space of the clusters identified by Giotto Analyzer in the pancreatic ductal adenocarcinoma (PDAC) tissue-CyCIF dataset, which covers multiple tissues, including pancreas, small intestine, and cancer cells (distance unit = 1 μm). g Heatmap showing the marker proteins for the identified cell clusters in f, h. Visualization in both expression and physical space of two selected windows (red squares in f) in the normal pancreas and small-intestinal regions. i, j Overlay of gene expression in both expression and physical space for the selected windows in h